Dear experts,

I am preparing my data for longitudinal statistical analysis following the steps in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics#LinearMixedEffectsModel.

I try running the following comand :

mris_preproc --qdec-long qdec/long.qdec.table-test.dat --target fsaverage --hemi lh --meas area --out output/lh.area.stack.mghmris_preproc --qdec-long qdec/long.qdec.table-test.dat --target fsaverage --hemi lh --meas area --out output/lh.area.stack.mgh

but it crashes because it looks for /fsaverage/label/lh.cortex.label

How can I create this label file?

Thank you very much in advance for your help, please find below the whole output.

Best, Diana

nsubjects = 25

INFO: turning on jacobican correction

tmpdir is output/tmp.mris_preproc.21054

/home/neuroimagen/AnalisisLongitudinalLMM

Log file is output/lh.area.stack.mris_preproc.log

lun jun 8 17:41:42 CEST 2020

setenv SUBJECTS_DIR /home/neuroimagen/AnalisisLongitudinalLMM/

cd /home/neuroimagen/AnalisisLongitudinalLMM

/usr/local/freesurfer/bin/mris_preproc --qdec-long qdec/long.qdec.table-test.dat --target fsaverage --hemi lh --meas area --out output/lh.area.stack.mgh

Linux localhost 4.4.0-179-generic #209-Ubuntu SMP Fri Apr 24 17:48:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

$Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

tmpdir is output/tmp.mris_preproc.21054

Src lh sphere.reg

Trg lh sphere.reg

---------------------------------------------------

#@# 1/25 100_001.long.100 lun jun 8 17:41:42 CEST 2020 --------------

-----------------------

mri_surf2surf --srcsubject 100_001.long.100 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval output/tmp.mris_preproc.21054/100_001.long.100.1.mgh --sval /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.area --jac --sfmt curv --noreshape --cortex

Source registration surface changed to sphere.reg

Target registration surface changed to sphere.reg

$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $

setenv SUBJECTS_DIR /home/neuroimagen/AnalisisLongitudinalLMM/

cd /home/neuroimagen/AnalisisLongitudinalLMM

sysname Linux

hostname localhost

machine x86_64

user neuroimagen

srcsubject = 100_001.long.100

srcval = /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.area

srctype = curv

trgsubject = fsaverage

trgval = output/tmp.mris_preproc.21054/100_001.long.100.1.mgh

trgtype =

srcsurfreg = sphere.reg

trgsurfreg = sphere.reg

srchemi = lh

trghemi = lh

frame = 0

fwhm-in = 0

fwhm-out = 0

label-src = lh.cortex.label

label-trg = lh.cortex.label

OKToRevFaceOrder = 1

UseDualHemi = 0

Reading source surface reg /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.sphere.reg

Loading source data

Reading curvature file /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.area

Reading source subject label mask lh.cortex.label

masking the input

Reading target surface reg /home/neuroimagen/AnalisisLongitudinalLMM//fsaverage/surf/lh.sphere.reg

Done

Using surf2surf_nnfr()

Mapping Source Volume onto Source Subject Surface with Jacobian Correction

surf2surf_nnfr_jac: building source hash (res=16).

Surf2SurfJac: 1st Forward Loop (163842)

Surf2SurfJac: 2nd Forward Loop (163842)

surf2surf_nnfr: building target hash (res=16).

Surf2SurfJac: Reverse Loop (149877)

Reverse Loop had 29625 hits

INFO: nSrcLost = 0

surf2surf_nnfr_jac() done

No such file or directory

mri_surf2surf: could not open label file /home/neuroimagen/AnalisisLongitudinalLMM//fsaverage/label/lh.cortex.label

nTrg121 = 141330, nTrgMulti = 22512, MnTrgMultiHits = 2.31596

nSrc121 = 115191, nSrcLost = 0, nSrcMulti = 34686, MnSrcMultiHits = 2.2567

Reading target space mask label lh.cortex.label

Invalid argument